Why are you so set on the development order being the correct one? It's not like they aren't all basically worked on at once anyway.
It mostly goes back to a long, heated argument on TVTropes on which order to go by, really. I figured the creator's word is more canon than anything else, so that's the side of the argument I fell under.
But, the argument didn't really go too well, I guess you could say. While Hasbro still used that numbering on their site and promotional materials, they don't leave much evidence to go by; iTunes changed the numbering after the fact (I'd much rather they'd just uploaded one or the other and stuck with it instead of twisting the knife like that); Shout! refuses to do boxsets or even ordered DVDs to help clarify; and the Hub tends to skip reairing the holiday episodes altogether (including "Luna Eclipsed", I've noticed, which seems odd since that was voted the most-popular episode in that poll they held). I'm generally too shy to go around correcting people without sufficient evidence, too, so there's also that. So... I'm still a bit bitter about the whole thing. Sorry...
The show's still enjoyable despite such minor things, though, and really, if this is the worst possible thing I can think of, then the overall show's doing a bang-up job. Season Two's arguably better than Season One, anyway, with more consistently good CMC episodes, lots of continuity callbacks, the short-lived Derpy shout-out, John de Lancie basically reprising one of my favorite
TNG characters, etc.
Oddly, Derpy's voice change didn't bother me that much - as cute as Tabitha's butch voice was, I thought the new voice fit better, even if the acting was a bit phoned-in. Speaking of:
I'm assuming Last Roundup is the altered one?
It's only Season One, but I'm going to assume when Season Two comes up that it will be. It doesn't really seem like the sort of thing Hasbro would just back down from after committing the time and money to make the change in the first place.